[English] 日本語
Yorodumi
- PDB-2wiw: Crystal structures of Holliday junction resolvases from Archaeogl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wiw
TitleCrystal structures of Holliday junction resolvases from Archaeoglobus fulgidus bound to DNA substrate
Components
  • 5'-D(*DC*DG*DG*DA*DT*DA*DT*DC*DC*DGP)-3'
  • HJC
KeywordsHYDROLASE/DNA / HYDROLASE-DNA COMPLEX / HYDROLASE DNA COMPLEX / TYPE II RESTRICTION ENDONUCLEASE / HOLLIDAY JUNCTION RESOLVASE / HYDROLASE / DNA BINDING PROTEIN
Function / homology
Function and homology information


crossover junction endodeoxyribonuclease / crossover junction DNA endonuclease activity / DNA recombination / DNA repair / magnesium ion binding / DNA binding
Similarity search - Function
Holliday junction resolvase Hjc / Holliday junction resolvase Hjc, archaeal / Archaeal holliday junction resolvase (hjc) / Trna Endonuclease; Chain: A, domain 1 - #10 / Trna Endonuclease; Chain: A, domain 1 / tRNA endonuclease-like domain superfamily / Restriction endonuclease type II-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
HEXANE-1,6-DIOL / DNA / Crossover junction endodeoxyribonuclease Hjc
Similarity search - Component
Biological speciesARCHAEOGLOBUS FULGIDUS (archaea)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCarolis, C. / Koehler, C. / Sauter, C. / Basquin, J. / Suck, D. / Toeroe, I.
CitationJournal: To be Published
Title: Crystal Structures of Holliday Junction Resolvases from Archaeoglobus Fulgidus Bound to DNA Substrate
Authors: Carolis, C. / Koehler, C. / Sauter, C. / Basquin, J. / Suck, D. / Toeroe, I.
History
DepositionMay 18, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HJC
B: HJC
C: 5'-D(*DC*DG*DG*DA*DT*DA*DT*DC*DC*DGP)-3'
D: 5'-D(*DC*DG*DG*DA*DT*DA*DT*DC*DC*DGP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,09510
Polymers37,4384
Non-polymers6576
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-19.4 kcal/mol
Surface area16870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.380, 82.860, 107.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.3748, 0.5075, -0.7759), (0.5454, -0.7974, -0.2581), (-0.7497, -0.3265, -0.5756)21.3, 14.84, 48.49
2given(-0.7673, 0.6118, -0.1923), (0.5937, 0.5642, -0.5737), (-0.2425, -0.5544, -0.7962)20.22, -7.501, 1.091

-
Components

#1: Protein HJC


Mass: 15674.213 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-136
Source method: isolated from a genetically manipulated source
Details: N-TERMINUS CONTAINS EXTRA RESIDUES AS A RESULT OF CLONING PROCEDURE
Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Strain: 4304 / Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Plasmid: PETM12 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): PLYSS / References: UniProt: O28314
#2: DNA chain 5'-D(*DC*DG*DG*DA*DT*DA*DT*DC*DC*DGP)-3'


Mass: 3045.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: SYNTHESIZED BY METABION GMBH, MARTINSRIED, GERMANY / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: Chemical
ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsINSERTED RESIDUES GTMG AT THE N-TERMINUS ARE A RESULT OF CLONING PROCEDURE. RESIDUES C1 AND D1 HAVE ...INSERTED RESIDUES GTMG AT THE N-TERMINUS ARE A RESULT OF CLONING PROCEDURE. RESIDUES C1 AND D1 HAVE THEIR 5'-PHOSPHATE GROUP REMOVED

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 42.76 %
Description: DECAMER PALINDROMIC DNA WAS MODELLED AS B-DNA IN COOT
Crystal growpH: 8.5
Details: 35 %(W/V) 1.6-HEXANEDIOL, 0.05 M TRIS.HCL PH=8.5, 0.005 M MAGNESIUM SULFATE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 8, 2008 / Details: PT COATED MIRRORS
RadiationMonochromator: SI (111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 27226 / % possible obs: 90.1 % / Observed criterion σ(I): 0 / Redundancy: 3.24 % / Biso Wilson estimate: 24.12 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.12
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.52 / % possible all: 73.9

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WCZ

2wcz


Resolution: 1.8→45.11 Å / SU ML: 0.21 / σ(F): 0.03 / Phase error: 22.11 / Stereochemistry target values: ML
Details: HYDROGENS WERE ADDED IN THE RIDING POSITIONS, BUT REMOVED FROM THE DEPOSITED COORDINATE FILE.
RfactorNum. reflection% reflection
Rfree0.2197 1391 5.1 %
Rwork0.1724 --
obs0.1747 27224 90.13 %
Displacement parametersBiso mean: 42.1 Å2
Baniso -1Baniso -2Baniso -3
1--2.3747 Å20 Å20 Å2
2--10.5832 Å20 Å2
3----8.2085 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1961 404 44 175 2584
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012518
X-RAY DIFFRACTIONf_angle_d1.2623477
X-RAY DIFFRACTIONf_dihedral_angle_d20.163977
X-RAY DIFFRACTIONf_chiral_restr0.078379
X-RAY DIFFRACTIONf_plane_restr0.006371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7992-1.86350.33271130.26242102X-RAY DIFFRACTION75
1.8635-1.93810.26841270.22552305X-RAY DIFFRACTION83
1.9381-2.02630.29321230.19772425X-RAY DIFFRACTION86
2.0263-2.13310.23781620.18282494X-RAY DIFFRACTION89
2.1331-2.26680.23171320.17452599X-RAY DIFFRACTION91
2.2668-2.44180.23571350.17622695X-RAY DIFFRACTION95
2.4418-2.68750.2371520.17042758X-RAY DIFFRACTION96
2.6875-3.07630.20481580.16912773X-RAY DIFFRACTION97
3.0763-3.87540.221360.15142839X-RAY DIFFRACTION97
3.8754-45.12530.18161530.16422843X-RAY DIFFRACTION93
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4931-0.722-0.37531.24270.34270.49570.01380.2057-0.235-0.10550.06920.22150.19880.1419-0.08010.23050.0126-0.04870.2442-0.01270.32210.403812.4204-29.5337
20.9662-0.10350.36221.37790.64563.3425-0.0010.1950.0173-0.16270.1019-0.0484-0.06040.1374-0.08880.1577-0.01220.00070.1493-0.00740.18715.554917.3886-41.1296
30.66940.02810.05620.0328-0.12890.49390.08250.0404-0.3091-0.2591-0.05310.19840.4179-0.0919-0.02280.24280.0197-0.01890.18470.00570.2734-4.7276.6392-20.6214
41.9118-0.13251.09831.7427-0.52962.31120.0093-0.3212-0.18750.18260.07120.0471-0.1323-0.0061-0.06790.18220.01720.00910.21320.02420.2185-2.577514.4631-9.5932
51.7468-0.4916-0.95612.92170.9041.63940.86590.6382-0.38780.1454-1.14710.12230.3427-1.1920.11060.4407-0.0046-0.03880.53470.01330.258912.2298-8.1162-6.5843
61.4635-1.33670.58014.41030.66872.40980.1526-0.14270.7001-0.22740.4326-1.2425-0.0881-0.169-0.40830.41460.0590.10690.3249-0.00990.430311.08825.03995.1915
71.03120.08180.00060.65540.47081.18960.27560.4487-0.11260.0290.1156-0.25250.08310.2375-0.30130.38350.0668-0.03720.21330.03980.29358.146-0.52076.6517
83.55281.26541.00382.4888-0.62350.80520.46431.94110.442-0.65940.37270.0338-0.6442-1.2189-0.64360.55760.20250.22190.64320.00960.41515.2087-1.5812-10.3859
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 5:35)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 36:124)
3X-RAY DIFFRACTION3(CHAIN B AND RESID 5:31)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 32:130)
5X-RAY DIFFRACTION5(CHAIN C AND RESID 1:5)
6X-RAY DIFFRACTION6(CHAIN C AND RESID 6:10)
7X-RAY DIFFRACTION7(CHAIN D AND RESID 1:6)
8X-RAY DIFFRACTION8(CHAIN D AND RESID 7:10)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more